'Omic' Technologies: Genomics, Transcriptomics, Proteomics and Metabolomics

The human mouth is one of the most __________ colonized parts of our bodies, harboring unique and diverse microbial communities

heavily

Mass spec is 3 functional units=

ion source, mass analyzer, detector system

Ion Source:

ionizes and transfer sample ions into a gas phase

Transcriptomics/ transcriptomes are?

mRNA

Metabolic dysregulation plays a key role in ____________ and _____________ of many prominent ___________ diseases particularly ____________ and _______

pathogenesis, progression, metabolic, obesity, diabetes

Proteins of interest are identified using a procedure named ___________ ______ ______________

peptide mass fingerprinting

During the process of _________________, the information stored in a gene's DNA is transferred to _________ in the nucleus

transcription, RNA

Limit of RNA seq: Upregulated ______________ does not always mean upregulated ___________

transcription, protein

RNA sequencing Data Project: evaluation of _________________ ________________ in a microbial cell induced by exposure to a ______

transcriptional modifications , drug

The _____________ is the set of all mRNA transcripts produced by a cell

transcriptome

RNA sequencing characterizes the ___________ involves conversion of _____ into complementary _______ (cDNA) followed by sequencing of the cDNA library

transcriptome, mRNA, DNA

A type of RNA called ___________ ___________ (_________) assembles the protein, one amino acid at a time

transfer RNA, tRNA

Mass spectrometry is a powerful analytical technique used to identify and quantify ____________ compounds in a sample by measuring the ________ of different molecules within a sample

unknown , mass

Human Genome Project determine the sequences of the ____ billion base pairs that make up human DNA

3

Human Genome Project identify all the approximate _________ genes in human DNA

30,000

Lifetime risks of breast cancer are as high as _____% among women with mutations in these genes, and lifetime risks of ovarian cancer are greater than _____% for carriers of __________ mutations and greater than ____% for carriers of __________ mutations.

80%, 40%, BRCA1, 20%, BRCA2

Proteomics/Proteome (protein) count=

>100000

Data analysis for Mass spectrometry:

A computer is required to control the instrument, acquire and manipulate data, and compare spectra to reference libraries. A mass spectrum of the molecule is produced displaying the result in a plot of ion abundance versus mass-to-charge ratio (m/z).

Candida albicans gene for actin?

ACT1

Genetic testing for _________ and _________ mutations has become an integral part of clinical practice for women with severe family histories of breast or ovarian cancer

BRCA1, BRCA2

The BRCA1 gene provides instructions for making a protein that acts as a _____________ suppressor which help prevent cells from growing and dividing too rapidly or in an uncontrolled way

BRCA1, tumore

Human Genome Project June 2000:

Completion of a working draft of the entire human genome

Sequencing an entire genome (all of an organism's DNA) is a complex task that requires breaking the ________ of the genome into many smaller pieces, sequencing the pieces, and assembling the sequences into a single long "__________"

DNA, consensus

mRNA, or messenger RNA that carries information from ________ in the __________ to the ___________ in the ___________, the sites of ___________ synthesis (translation) in the cell

DNA, nucleus, ribosomes, cytoplasm, protein

Limit of RNA seq: ________ positives can occur and therefore, a secondary method such as ____-__________ is needed to confirm results.

False, qRT-PCR

Data analysis RNA sequencing data:

Fold increase in expression of a gene in cells grown with the drug (gr 2) compared to expression in cells with no drug (gr 1).. 4 fold increase in the expression of ureE = the drug significantly increased expression of the gene.

___________ studies has provided a useful framework for mapping and studying specific genetic variants contributing to diseases

Genomic

Bioinformatics Data analysis:

Given the enormous amount of data generated from omics studies, sophisticated bioinformatics and statisticians are fundamental.

Human Genome Project April 2003:

HGP sequencing is completed

Mutation example: sickle-cell disease is caused by a mutation of a single base pair in the gene that codes for one of the polypeptides of hemoglobin=

a change in a single nucleotide from T to A in the DNA temple leads to an abnormal protein

The first major sequencing project was the _________ ___________ ____________

Human Genome Project

______________ sequencing works by simultaneously identifying DNA bases, as each base emits a unique ______________ signal, and adding them to a _______ ________ chain. The system automatically identifies the _____________ ______________- and saves the information on the computer.

Illumina, fluorescent, nucleic acid, nucleotide sequence

Benefits of Genome Research:

Improve diagnosis of disease, Detect genetic predispositions to disease, Use gene therapy, Design "custom drugs" (pharmacogenomics) based on individual genetic profiles, Rapidly detect and treat pathogens in clinical practice, Identify potential suspects whose DNA may match evidence left at crime scene, Exonerate persons wrongly accused of crimes, Establish paternity and other family relationships, Match organ donors with recipients in transplant programs

_____________ levels and relative ratios reflect ___________ function, and out of normal range perturbations are often indicative of disease

Metabolite, metabolic

Metabolomics:

Involves the comprehensive and simultaneous profiling and quantification of multiple chemicals and small molecule metabolites such as amino acids, fatty acids, carbohydrates, or other products of cellular metabolic functions.

Proteomics has been revolutionized by __________ -____________-based methods which have been adapted for ______-_______________ analyses of thousands of proteins in cells

Mass Spectrometry, high-throughput

_____-__________ ________________ sequencing or _________-__________ sequencing, describe a number of different modern sequencing technologies.

Next-generation automated, high-throughput

Human Genome Project in 1990:

Project initiated as joint effort of U.S. Department of Energy and the National Institutes of Health

Proteome:

Proteins expressed by the genome.

Both _______ and _______ are made up of a chain of ____________ ___________, but they have slightly different ______________ properties.

RNA, DNA, nucleotide bases, chemical

________ __________ (RNA) is a polymeric molecule essential in various biological roles in coding

Ribonucleic acid

________________ _____________________ sequencing, in which total DNA is sequenced, can provide additional resolution for distinguishing genetically close microbial species

Shotgun metagenomics

Metabolome:

The collection of all metabolites in a biological organism, which are the end products of its gene expression

Genome:

The entire DNA sequence of a particular species

Basic principle of mass spec

The process involves the production of ions from the sample by electron ionization, which are then characterized by their mass to charge ratios (m/z) and relative abundances.

Genomics

The study of genes and their function.

Each sequence of ________ bases, called a ___________, usually codes for one particular amino acid (the building blocks of proteins).

Three, codon

____________, the second step in getting from a gene to a protein, takes place in the _____________ where the __________ interacts with a ________________ complex called a _____________, which "reads" the sequence of mRNA bases.

Translation, cytoplasm, mRNA, specialized, ribosome

Candida albicans ACT1 codes for what?

actin

mutations can change the _______ _______ _____________ of proteins

amino acid sequences

tRNA, or transfer RNA, that ferry ________ _________ to the ribosome to be _______________

amino acids, assembled

The microbiome can be profiled by _____________ and then ___________________ certain _______________ regions of the bacterial ___________ rRNA genes followed by _____________ the sequences into operational taxonomic units

amplifying, sequencing, hypervariable, 16S, clustering

Bioinformatics involves?

biology, computer science, and information technology and basically provides computational tools to make sense and predictions from genomic, proteomic, metabolomic, and other omic data.

Mass Spectrometry is used to analyze ______________ like peptides, lipids, saccharides, or other organic macromolecules

biomolecules

Inherited mutations in BRCA1 and BRCA2 increase the risk of _________ and _________ cancers

breast, ovarian

metabolomics is also applied to predict ________ and incidents of ____________ events

cancer , cardiovascular

oral diseases arise as a result of a __________ in the proportion of certain species with greater ____________ potential within the indigenous __________

change, pathogenic, flora

Proteomics: The scientific discipline of?

characterizing and analyzing peptide abundance, protein interactions, and protein modifications of an organism.

The addition of "omics" to a molecular term implies a?

comprehensive, or global, assessment of a set of molecules in a specific biological sample.

Human Genome Project store this information in ____________

databases

Detector System:

detects the ions emerging from the analyzer and measures their relative abundance.

DNA sequencing is the process of?

determining the sequence of nucleotide bases (As, Ts, Cs, and Gs) in a piece of DNA.

Accumulation of these microbial populations within the _____________ community induces _____________, causing destruction of oral tissue

dysbiotic, inflammation

However, in addition to metabolic disorders, _______________ metabolism is being recognized as a major contributor to diseases such as __________, ___________ disorders, _______________ diseases and ____________ pathologies

dysregulated, cancer, cognitive, cardiovascular, respiratory

The journey from gene to protein is complex and tightly controlled within ________ ________?

each cell.

Human Genome Project was a big consortium began collaborative efforts in __________ to sequence the ________ human genome. The project was nominally completed in 2003, costing $______ ___________ and ____ years of work by labs around the world.

entire, 1990, 2003, 2.7 billion, 13

Sequencing, thanks to new methods that have been developed over the past two decades, genome sequencing is now much __________ and _______ expensive

faster, less

Together, transcription and translation are known as _________ _____________

gene expression

Transcriptomics: The study of?

gene expression.

Genomics: The study of?

genes and their function.

DNA sequencing allows us to detect _____________ ___________- to disease

genetic predispositions

Genomics is a branch of biotechnology aims to understand the structure of the __________, including the _____________ genes, ______________ the DNA of genes, collecting genomic __________ within a _____________ and organizing the results in databases for application of the data in medicine or biology.

genome, mapping, sequencing, variations, population

Transcriptomics examines RNA levels ___________-__________, both qualitatively (which transcripts are present) and quantitatively (how much of transcript is expressed)

genome-wide

Principle of RNA-Sequencing

mRNA is extracted from the cell, fragmented and copied into stable ds-cDNA (blue), The cDNA is sequenced using high-throughput sequencing methods, Sequences are aligned to a reference genome sequence to reconstruct which genome regions are being transcribed

Three major types of RNA:

mRNA, rRNA, tRNA

The type of RNA that contains the information for making a protein is called _______________ ____________ (_________) because it carries the information, or message, from the DNA out of the nucleus into the cytoplasm

messenger RNA, mRNA

When a gene is expressed in a cell, it generates ______________ _________ (mRNA); _______expressed genes generate more mRNA than ___________-expressed gene

messenger RNA, over, under

Metabolomics: The the study of?

metabolites (e.g., calcium, cholesterol, glucose) present.

Periodontitis is hypothesized to be a "________________" where the microbial populations shift from Gram-_________ __________bacteria to Gram-______ _________

microbial-shift disease positive aerobic, negative anaerobes

Human skin, mucosal surfaces, and the gut are colonized by microorganisms, including bacteria, viruses, and fungi, collectively known as the _____________ (and their genes constituting the microbiome)

microbiota

Microbiomics is a fast-growing field in which all the ______________ of a given community are investigated ___________

microorganisms , together

The _______________ sequence is the most fundamental level of knowledge of a gene or genome

nucleotide

Bioinformatics examples of information that you can access:

nucleotide sequence, protein sequence, exon/intron structure, predicted molecular weight of the protein, pI, protein targeting sequences, expression pattern, T-DNA insertion mutants, BLAST sequence alignments.

Proteomics supplements the other "________" technologies such as genomic and transcriptomics to expound the identity of proteins of an organism.

omics

the oral microbiome is crucial in maintaining?

oral health

Nucleotide sequence is the blueprint that contains the instructions for building an ___________ and no understanding of genetic ______________ or evolution could be complete without obtaining this information

organism, function

Therefore, perturbations that disrupt oral homeostasis or "dysbiosis" may lead to the _______________ of species with pathogenic potential, and in turn development of oral __________

overgrowth, disease

Structural proteomics:refers to the development and application of experimental approaches to define the?

primary, secondary, and tertiary structure of proteins.

DNA gene sequence is the recipe that makes?

protein

The conventional methodology for protein analysis includes:

protein extraction, purification fractionation by biochemical approaches followed by enzymatic digestion (usually trypsin), peptide extraction, and Mass Spectrometry analysis.

Functional proteomics: refers to the development and application of experimental approaches to assess?

protein function by making use of the information provided by structural genomics.

rRNA, or ribosomal RNA, serve as structural components of _______-____________ structures known as ____________

protein-making, ribosomes

Genes contain the information needed to make functional molecules called ___________?

proteins

Proteomics is used to identify _________ obtained from a biological sample which can be done by __________ __________ sequencing using a ________ spectrometer and matching the data to a _________ database

proteins, amino acid, mass, protein

Nowadays, high-throughput techniques including total __________ analysis are employed to study protein network biology

proteome

Microbiomics allow accurate ____________ determination of microbiota that can be correlated with disease

quantitative

RNA sequencing (RNA-Seq) is a highly _____________ and ____________ tool for measuring expression across the _______________ and it is increasingly the method of ___________ for studying the transcriptome

sensitive, accurate, transcriptome, choice

Mass analyzer:

separates ions according to their mass-to-charge ratio (m/z)

Protein assembly continues until the ribosome encounters a "________" codon (a sequence of three bases that does not code for an amino acid)

stop

BRCA1, BRCA2 do what when healthy?

stop proliferation of damaged cells

Bioinformatics is a new discipline which has emerged because of the need to?

store and analyze vast amounts of nucleic acid and protein sequence data.

Limit of RNA seq: Results may not be consistent among different ________ of the same _________ and _______________ conditions.

strains, species environmental

The Omics field has been driven largely by _____________ advances that have made possible cost-efficient, _______-_________ _____________ of biologic molecules

technological, high-throughput analysis

The human microbiome is enormously complex; for example

the gut contains roughly 100 trillion bacteria from 1000 different species and 700 bacterial species have been identified in the oral cavity.

Proteomics: The study of?

the proteome, which corresponds to all expressed proteins.

Protein synthesis consists of two major steps:

transcription and translation.

Genomics/genome (Gene) how many?

~35000

Metabolomics count=

~5000